mdadash.backend.kernel.core

Kernel core where MDAnalysis code runs

Functions

init_n_universes(data)	Initialize n universes in UniverseManager
run_notebooks(notebooks)	Run notebooks from loaded state file

Classes

BufferFrameIteratorIndices()	Iterable over the frames of a trajectory buffer listed as a sequence of indices.
BufferedTrajectory(trajectory, buffer_size)	Buffered Trajectory
CommHandler()	Comm Handler
UniverseManager(_comms)	Universe Manager

class mdadash.backend.kernel.core.BufferFrameIteratorIndices

Bases: FrameIteratorBase

Iterable over the frames of a trajectory buffer listed as a sequence of indices. This is very similar to FrameIteratorIndices in MDAnalysis, but without rewind() and __getitem__ as they aren’t needed here.

property frames

class mdadash.backend.kernel.core.BufferedTrajectory(trajectory: <property object at 0x7cf19b8dad90>, buffer_size: int)

Bases: object

Buffered Trajectory

This class is a wrapper for the trajectory reader and provides buffered access to the last n timesteps.

trajectory[index] can be used to access individual frames. Index values can range from 0 to the configured batch size.

property buffer_size

check_slice_indices(start, stop, step)

property n_frames

next()

Iterate next frame and copy timestep into buffer

class mdadash.backend.kernel.core.CommHandler

Bases: object

Comm Handler

This class is responsible for handling all the communication to and from this kernel. This is the class that interfaces with the KernelManager on the server side.

register_handler(msg_type: str, handler_func: callable) → None

Register a handler function for a message type

Parameters:

• msg_type (str) – A message type to identify the handler

• handler_func (callable) – The handler function to invoke when a message with this message type is received

send(msg: dict) → None

Send a message (response) back on the comm

Parameters:

msg (dict) – A generic message dictionary

class mdadash.backend.kernel.core.UniverseManager(_comms: CommHandler)

Bases: object

Universe Manager

This class is responsible for managing all MDAnalysis universes. It has handlers to interact with the MD simulation. These handlers are invoked by comm messages sent from the server.

This also provides an iterable and indexable access to the individual universes.

connect_to_simulations(universe_configs: list[dict]) → None

Connect to MD simulations

Parameters:

universe_configs (list[dict]) – A list of configurations for universe(s) creation. Each dict has universe related config like topology, trajectory, imdclient params, user-defined kwargs etc

disconnect_from_simulations(_data: dict) → None

Disconnect from MD simulations

init_n_universes(n: int) → None

Initialize array for n universes

Parameters:

n (int) – Number of universes to initialize

pause_simulations(_data: dict) → None

Pause MD simulations

resume_simulations(_data: dict) → None

Resume MD simulations

mdadash.backend.kernel.core.init_n_universes(data: dict) → None

Initialize n universes in UniverseManager

mdadash.backend.kernel.core.run_notebooks(notebooks: dict) → None

Run notebooks from loaded state file